.Dd Oct 10, 2019
.Os "Open Babel" 3.1
.Dt obrotate 1 URM
.Sh NAME
.Nm obrotate
.Nd "batch-rotate dihedral angles matching SMARTS patterns"
.Sh SYNOPSIS
.Nm
.Ar SMARTS-pattern
.Ar filename
.Ar atom1
.Ar atom2
.Ar atom3
.Ar atom4
.Ar angle
.Sh DESCRIPTION
The
.Nm
program rotates the torsional (dihedral) angle of a
specified bond in molecules to that defined by the user. In other
words, it does the same as a user setting an angle in a molecular
modelling package, but much faster and in batch mode (i.e. across
multiple molecules in a file).
.Pp
The four atom IDs required are indexes into the SMARTS pattern, which
starts at atom 0 (zero). The angle supplied is in degrees. The two
atoms used to set the dihedral angle
.Ar atom1
and
.Ar atom4
do not need
to be connected to the atoms of the bond
.Ar atom2
and
.Ar atom3
in any way.
.Pp
The order of the atoms matters -- the portion of the molecule attached
to
.Ar atom1
and
.Ar atom2
remain fixed, but the portion bonded to
.Ar atom3
and
.Ar atom4
moves.
.Sh EXAMPLES
Let's say that you want to define the conformation of a large number
of molecules with a pyridyl scaffold and substituted with an aliphatic
chain at the 3-position, for example for docking or 3D-QSAR purposes.
.Pp
To set the value of the first dihedral angle to 90 degrees:
.Dl "obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90"
.Pp
Here 6 and 7 define the bond to rotate in the SMARTS pattern, i.e.,
c1-C and atoms 5 and 8 define the particular dihedral angle to
rotate.
.Pp
Since the atoms to define the dihedral do not need to be directly
connected, the nitrogen in the pyridine can be used:
.Dl "obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90"
.Pp
Keep the pyridyl ring fixed and moves the aliphatic chain:
.Dl "obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90"
.Pp
Keep the aliphatic chain fixed and move the pyridyl ring:
.Dl "obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90"
.Sh SEE ALSO
.Xr obabel 1 ,
.Xr obchiral 1 ,
.Xr obfit 1 ,
.Xr obgrep 1 ,
.Xr obprop 1 .
.Pp
.Pp
The web pages for Open Babel can be found at:
\%<\fBhttp://openbabel.org/\fR>
.Pp
A guide for constructing SMARTS patterns can be found at:
\%<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR>
.Sh AUTHORS
The obgrep program was contributed by
.An Fabien Fontaine
.Pp
.An -nosplit
Open Babel is developed by a cast of many, including current maintainers
.An Geoff Hutchison ,
.An Chris Morley ,
.An Michael Banck ,
and innumerable others who have contributed fixes and additions.
For more contributors to Open Babel, see
\%<\fBhttp://openbabel.org/wiki/THANKS\fR>
.Sh COPYRIGHT
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
.br
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison and
other contributors.
.Pp
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
.Pp
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
